The formation of gaps in the endothelium is a crucial process underlying both cancer and immune cell extravasation, contributing to the functioning of the immune system during infection, the unfavorable development of chronic inflammation and tumor metastasis. Here, we present a stochastic-mechanical multiscale model of an endothelial cell monolayer and show that the dynamic nature of the endothelium leads to spontaneous gap formation, even without intervention from the transmigrating cells. These gaps preferentially appear at the vertices between three endothelial cells, as opposed to the border between two cells. We quantify the frequency and lifetime of these gaps, and validate our predictions experimentally. Interestingly, we find experimentally that cancer cells also preferentially extravasate at vertices, even when they first arrest on borders. This suggests that extravasating cells, rather than initially signaling to the endothelium, might exploit the autonomously forming gaps in the endothelium to initiate transmigration. Author summary Transmigration of immune cells into and out of the blood vessels is a crucial process for the functioning of the immune system during infections and acute inflammations, and aberrant transmigration may contribute to chronic inflammations. Likewise, cancer metastasis critically depends on intra-and extravasation of cancer cells through the endothelium. While much research investigated the role of immune or cancer cells in signaling to the endothelium, facilitating effective transmigration, and some work uncovered a role of passive mechanical properties such as stiffness during transmigration, little is known about the active role the endothelium itself plays during such processes. Our computational model, together with new data, highlights the dynamic nature of endothelial cells, leading to gap formations through mechanical processes within the endothelium, without influence of cancer or immune cells. Thus, our results highlight the need to take the active mechanics of the endothelium into account when devising strategies to overcome the adverse effects of endothelial gap formation during inflammation or cancer.